PXD023094

PXD023094 is an original dataset announced via ProteomeXchange.

Title	Three-in-one simultaneous extraction of proteins, metabolites and lipids for multi-omics
Description	Elucidation of complex molecular networks requires integrative analysis of molecular features and changes at different levels of information flow and regulation. Accordingly, high throughput functional genomics tools such as transcriptomics, proteomics, metabolomics and lipidomics have emerged to provide system-wide investigations. Unfortunately, analysis of different types of biomolecules requires specific sample extraction procedures in combination with specific analytical instrumentation. The most efficient extraction protocols often only cover a restricted type of biomolecules due to their different physicochemical properties. Therefore, several sets/aliquots of samples are needed for extracting different molecules. Here we adapted a bi-phasic fractionation method to extract proteins, metabolites and lipids from the same sample (3-in-1) for liquid chromatography-tandem mass spectrometry (LC-MS/MS) multi-omics. To demonstrate utility of the improved method, we used bacteria-primed Arabidopsis leaves to generate multi-omics datasets from the same sample. In total, we were able to analyze 1849 proteins, 1967 metabolites and 424 lipid species in single samples. The molecules cover a wide range of biological and molecular processes. Our results have shown the clear advantages of the multi-omics method, including sample conservation, high reproducibility and tight correlation between different types of biomolecules.
HostingRepository	PRIDE
AnnounceDate	2021-08-17
AnnouncementXML	Submission_2021-08-17_21:49:53.265.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lisa David
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-13 11:10:19	ID requested
1	2021-08-17 06:02:43	announced
⏵ 2	2021-08-17 21:49:54	announced	2021-08-18: Updated publication reference for PubMed record(s): 33936167.

Kang J, David L, Li Y, Cang J, Chen S, Three-in-One Simultaneous Extraction of Proteins, Metabolites and Lipids for Multi-Omics. Front Genet, 12():635971(2021) [pubmed]

submitter keyword: Arabidopsis thaliana, Systemic Acquired Resistance, multi-omics, proteomics, metabolomics, lipidomics

Sixue Chen
contact affiliation	Biology Department University of Florida
contact email	schen@ufl.edu
lab head
Lisa David
contact affiliation	University of Florida
contact email	lisaidavid@ufl.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/08/PXD023094

PRIDE project URI

• PRIDE
  1. PXD023094
     1. Label: PRIDE project
     2. Name: Three-in-one simultaneous extraction of proteins, metabolites and lipids for multi-omics